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opencc-by-4.0Jan 2024View details →

Linking diet switching to reproductive performance across populations of two Critically Endangered mammalian herbivores

Data associated with Harvey Sky, N., Britnell, J., Antwis, R. et al. Linking diet switching to reproductive performance across populations of two critically endangered mammalian herbivores. Commun Biol 7, 333 (2024). https://doi.org/10.1038/s42003-024-05983-3 The data deposited here includes raw metabarcoding output fasta files and some processed metabarcoding and sample data in xslx files. We include a more detailed description of each file below. Data regarding Kenyan black rhino and Grevy’s zebra are treated as sensitive and confidential. There are therefore restrictions on the data that we can make available. Due to these confidentiality considerations, the sample data stored here does not include locations of sample collection within each reserve for either species, or the identity or breeding data for black rhino. It also only includes the final processed values for NDVI and rainfall. The remote sensing data is available from the repositories cited in the methods, but we cannot provide the shapefiles or other data used to calculate the final values for each sample.  Raw fasta files_plants.zip A zipped folder containing the raw fasta files which were the output from the MiSeq sequencing of dietary plants in the faecal samples for both black rhino and Grevy's zebra. Within the zipped folder, the first part of the title of each fasta.gz file is the sample code (S1, S2, S3 etc), which allows you to cross reference these files with the sample data and processed sequencing data in the xslx files. Files with R1 in the title are foward reads, and R2 are reverse reads.  Raw fasta files_bacteria.zip A zipped folder containing the raw fasta files which were the output from the MiSeq sequencing of microbiome bateria in the faecal samples for both black rhino and Grevy's zebra. Within the zipped folder, the first part of the title of each fasta.gz file is the sample code (S1, S2, S3 etc), which allows you to cross reference these files with the sample data and processed sequencing data in the xslx files. Files with R1 in the title are foward reads, and R2 are reverse reads.  Sample data and processed metabarcoding data_Black rhino.xlsx Sample data tab The data that we are able to share that is associated with each black rhino sample. SampleID - The code used to identiy each sample which allows it be cross-referenced with other tabs and the fasta files.  IndividualID - We are not able to share rhino names or other identifiers, but we have given each individual a unique number so that it can be seen which samples came from the same individuals.  NDVI - Mean NDVI of each individual's area of utilisation in the 10-day period  within which the sample was collected. The method used to calculate this is described in the methods of the article.  Rainfall - Cumulative rainfall over the 30 days previous to sample collection for the 0.05 degree pixel under the sample. The method used to calculate this is described in the methods of the article.  Season - Post is the post-rain sampling season June-July 2018. Pre is the pre-rain sampling season January-March 2019.  Reserve - The reserve that the sample was collected on.  Date - The date of sample collection.  Dietary breadth - Shannon-Wiener index of dietary alpha diversity. The method used to calculate this is described in the methods of the article. NA signifies that the number of reads returned for that sample was under the threshold that signified sequencing failure for the dietary plant metabarcoding. Poaceae, Fabaceae, Ebenaceae - The relative abundance of each of these three dietary plant families that were the focus of our analyses. The method used to calculate these is described in the methods of the article. NA signifies that the number of reads returned for that sample was under the threshold that signified sequencing failure for the dietary plant metabarcoding. Bacteria numbers of reads The number of reads assigned to each bacterial ASV found in each sample.  Bacteria sequences and reads The sequence of each ASV, and the taxa assigned to each sequence in the microbiome metabarcoding. The method for taxonomic assignment is described in the methods of the article.  Plant numbers of reads The number of reads assigned to each dietary plant ASV found in each sample.  Plant sequences and reads The sequence of each ASV, and the taxa assigned to each sequence in the dietary plant metabarcoding. The method for taxonomic assignment is described in the methods of the article.    Sample data and processed metabarcoding data_Grevy's zebra.xlsx Sample data tab The data that we are able to share that is associated with each Grevy's zebra sample. Sample ID - The code used to identiy each sample which allows it be cross-referenced with other tabs and the fasta files.  NDVI - Mean NDVI of each individual's area of utilisation in the 10-day period  within which the sample was collected. The method used to calculate this is described in the methods of the article.  Rainfall - Cumulative rainfall over the 30 days previous to sample collection for the 0.05 degree pixel under the sample. The method used to calculate this is described in the methods of the article.  Reserve - The reserve that the sample was collected on.  Season - Post is the post-rain sampling season July-August 2018. Pre is the pre-rain sampling season January-February 2019.  Date - The date of sample collection.  Dietary breadth - Shannon-Wiener index of dietary alpha diversity. The method used to calculate this is described in the methods of the article.  Poaceae, Fabaceae - The relative abundance of each of these two dietary plant families that were the focus of our analyses. The method used to calculate these is described in the methods of the article. NA signifies that the number of reads returned for that sample was under the threshold that signified sequencing failure for the dietary plant metabarcoding. Indigofera - The relative abundance of each of this Fabaceae genus was included in our analyses. The method used to calculate these is described in the methods of the article. NA signifies that the number of reads returned for that sample was under the threshold that signified sequencing failure for the dietary plant metabarcoding. Bacteria numbers of reads The number of reads assigned to each bacterial ASV found in each sample.  Bacteria sequences and reads The sequence of each ASV, and the taxa assigned to each sequence in the microbiome metabarcoding. The method for taxonomic assignment is described in the methods of the article.   Plant numbers of reads The number of reads assigned to each dietary plant ASV found in each sample.  Plant sequences and reads The sequence of each ASV, and the taxa assigned to each sequence in the dietary plant metabarcoding. The method for taxonomic assignment is described in the methods of the article.

opencc-by-4.0Apr 2013View details →

Figure 1 in Effects of a Spirulina platensis-based diet on zebrafish female reproductive performance and larval survival rate

Figure 1. - Percentage of spawn according to the size of the clutch. Error bars represents standard error mean (SEM). **: p-value ≤ 0.01; FG: Flakes Group; SG: Spirulina platensis Group.

opencc-by-4.0Apr 2013View details →

Figure 3 in Effects of a Spirulina platensis-based diet on zebrafish female reproductive performance and larval survival rate

Figure 3. - Larvae survival rate (mean +/- SEM) when larvae are fed with 3 different diets, starting from 7 days post fertilization (0 hour).

opencc-by-4.0Apr 2013View details →

Figure 2 in Effects of a Spirulina platensis-based diet on zebrafish female reproductive performance and larval survival rate

Figure 2. - HT50 represents the time required to observe 50% hatched embryos in the two diet groups spawned one (Day 1), five (Day 5) and ten (Day 10) days after diet change. **: p-value ≤ 0.01; ***: p-value ≤ 0.001. Standard errors are represented. FG: Flakes Group; SG: Spirulina platensis Group.

opencc-by-4.0Feb 2023View details →

Reproduction package for the paper "The Impact of Hard and Easy Negative Training Data on Vulnerability Prediction Performance"

This Reproduction package contains the datasets, code and results for the paper "The Impact of Hard and Easy Negative Training Data on Vulnerability Prediction Performance" for other researchers to use for reproducing or improving our work.

dryad40/100

Sex-specific variation in thermal sensitivity has multiple negative effects on reproductive trait performance

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publicMar 2025View details →

dryad40/100

Measures of male reproductive performance across mating events

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publicMar 2024View details →

opencc-zeroNov 2020View details →

Colorful traits in avian females, individual condition, reproductive performance, and male mate preferences: A meta-analytic approach

Colorful ornaments in females are suggested to have evolved and be maintained by sexual selection. Although several studies have evaluated this idea evidence is still equivocal. Results from empirical studies have been compilated in reviews, but quantitative analyses have seldom been performed. Here, using a meta-analytic approach, we show that evidence from empirical studies conducted in birds, supports the ideas that colorful female ornaments are positively associated with individual condition, reproductive performance, and male-mate preferences. Hence, females' colorful traits, in birds, likely evolved and are maintained by sexual selection.

opencc-zeroDec 2017View details →

Data from: Physiological predictors of reproductive performance in the European Starling (Sturnus vulgaris)

Background: It is widely assumed that variation in fitness components has a physiological basis that might underlie selection on trade-offs, but the mechanisms driving decreased survival and future fecundity remain elusive. Here, we assessed whether physiological variables are related to workload ability or immediate fitness consequences and if they mediate future survival or reproductive success. We used data on 13 physiological variables measured in 93 female European starlings (Sturnus vulgaris) at two breeding stages (incubation, chick-rearing), for first-and second-broods over two years (152 observations). Results: There was little co-variation among the physiological variables, either in incubating or chick-rearing birds, but some systematic physiological differences between the two stages. Chick-rearing birds had lower hematocrit and plasma creatine kinase but higher hemoglobin, triglyceride and uric acid levels. Only plasma corticosterone was repeatable between incubation and chick-rearing. We assessed relationships between incubation or chick-rearing physiology and measures of workload, current productivity, future fecundity or survival in a univariate manner, and found very few significant relationships. Thus, we next explored the utility of multivariate analysis (principal components analysis, Mahalanobis distance) to account for potentially complex physiological integration, but still found no clear associations. Conclusions: This implies either that a) birds maintained physiological variables within a homeostatic range that did not affect their performance, b) there are relatively few links between physiology and performance, or, more likely, c) that the complexity of these relationships exceeds our ability to measure it. Variability in ecological context may complicate the relationship between physiology and behavior. We thus urge caution regarding the over-interpretation of isolated significant findings, based on single traits in single years, in the literature.

opencc-by-4.0Dec 2018View details →

Plate 1 in Reproduction Performance, Serum Biochemical and Growth Indices of Grower Rabbits (Oryctolagus cuniculus) fed Sheabutter (Vitellaria paradoxa C.F. Gaertn.) Nut Meal

Plate 1. Uterus of the dead doe showing four embryos

opencc-zeroJan 2022View details →

Supplementary data to "Alternative reproductive tactics are associated with sperm performance in invasive round goby from two different salinity environments"

During male-male competition, evolution can favor alternative reproductive tactics. This often results in a dominant morph that holds a resource, such as a nest for egg laying, competes with a smaller sneaker morph that reproduces by stealing fertilizations. The salinity environment can influence male growth rates, e.g. via osmoregulatory costs, which in turn may influence the use of sneaker tactics for small males competing for mating opportunities. Salinity can also affect sperm directly; however, little is known of how salinity influences sneaker tactics through sperm performance. We sampled males of the invasive round goby (Neogobius melanostomus) from two environments, a freshwater river and a brackish estuary. This fish has two male morphs: nest-holding dark males and non-nest-holding light males. We examined the role of water salinity of 0, 8 and 16 on sperm performance and found that in estuarine males, a salinity of 0 reduced sperm velocity compared to a salinity of 8 and 16. Riverine males had low velocity in all salinities. Sperm viability also decreased by over 30 % in 0 salinity, compared to 8 and 16, for fish from both environments. Gobies produce ejaculate contents in specialized glands that could in theory shield sperm in an adverse environment. However, gland contents did not improve sperm performance in our tests. Body mass and age estimates indicate that riverine males invested more in somatic growth compared to estuarine males. Estuarine light morph males had a high enough gonadosomatic index to indicate sneaker tactics. We propose that when sperm performance is low, such as for the riverine males, sneaker tactics are ineffective, and will be selected against or phenotypically suppressed. Instead, we interpret the increased investment in somatic growth found in riverine males as a life-history decision that is advantageous when defending a nest in the next reproductive season.

opencc-zeroJun 2024View details →

Genotypic data from: Lab-based evaluation of the reproductive performance of trojan (MYY) brook trout (Salvelinus fontinalis)

Evaluating the efficacy of the use of trojan male brook trout with two Y chromosomes (MYY) requires a better understanding of reproductive performance. We measured the reproductive performance of hatchery age-0 and age-1 MYY brook trout compared to hatchery XY males using laboratory crosses. Offspring of XY males had higher survival than offspring of age-1 MYY one day post-fertilization but not offspring of age-0 MYY. We found no detectable differences in survival from eyed-egg to the juvenile-fry stage. However, size-at-age differed, where offspring of age-0 MYY were 3.6% smaller in length and 25.2% smaller in weight than those of XY males. For crosses fertilized by both MYY and XY males, we found that a significantly higher proportion of offspring within families were sired by MYY versus XY males. These results show, under controlled conditions, evidence for possible fitness advantage for MYY under sperm competition, but a possible fitness disadvantage associated with early growth of their offspring. Overall, our results hold promise for the use of MYY brook trout to serve as an effective eradication tool.

opencc-zeroAug 2021View details →

Colorful traits in female birds relate to individual condition, reproductive performance, and male mate preferences: A meta-analytic approach dataset

Colorful traits in females are suggested to have evolved and be maintained by sexual selection. Although several studies have evaluated this idea, support is still equivocal. Evidence has been compiled in reviews, and a handful of quantitative synthesis have explored evidence of the link between condition and specific color traits in males and females. However, understanding the potential function of females' colorful traits in sexual communication has not been the primary focus of any of those previous studies. Here, using a meta-analytic approach, we find that evidence from empirical studies in birds supports the idea that colorful female ornaments are positively associated with residual mass and immune response, clutch size, and male-mate preferences. Hence, colorful traits in female birds likely evolved and are maintained by sexual selection.

FIGURE 5 in Effects of six greenhouse cucumber cultivars on reproductive performance and life expectancy of Tetranychus turkestani (Acari: Tetranychidae)

FIGURE 5: Ward's dendrogram of six greenhouse cucumber cultivars based on reproductive parameters of Tetranychus turkestani on six greenhouses cucumber cultivars. A- favorite host plant for the reproduction of the strawberry spider mite, B- partially unpleasant group for the reproduction of this mite, B1- comparatively semi-resistant group and B2 - partly more resistant compared to cultivars in the B1 cluster.

FIGURE 3 in Effects of six greenhouse cucumber cultivars on reproductive performance and life expectancy of Tetranychus turkestani (Acari: Tetranychidae)

FIGURE 3: Mean (±SE) hatching rate of Tetranychus turkestani reared on six greenhouse cucumber cultivars. Means followed by same letters in each column are not significantly different (P <0.05, LSD).

FIGURE 2 in Effects of six greenhouse cucumber cultivars on reproductive performance and life expectancy of Tetranychus turkestani (Acari: Tetranychidae)

FIGURE 2: Mean (±SE) oviposition rate Tetranychus turkestani reared on six greenhouse cucumber cultivars. Means followed by same letters in each column are not significantly different (P <0.05, LSD).

FIGURE 4 in Effects of six greenhouse cucumber cultivars on reproductive performance and life expectancy of Tetranychus turkestani (Acari: Tetranychidae)

FIGURE 4: Age – stage reproductive value (vxj) of Tetranychus turkestani fed on six greenhouse cucumber cultivars. Age reproductive value of Tetranychus turkestani in each stage was shown by solid black circle (egg), solid white square (larva), solid black triangle up (nymph 1), solid white diamond (nymph 2), solid white circle (female) on six greenhouse cucumber cultivars. a- cultivar Puia, bcultivar Hedieh, c- cultivar Milad Jadid, d- cultivar Milad Ghadim, e- Khasib, f- Negin.

FIGURE 1 in Effects of six greenhouse cucumber cultivars on reproductive performance and life expectancy of Tetranychus turkestani (Acari: Tetranychidae)

FIGURE 1: Age-stage life expectancy (exj) of Tetranychus turkestani fed on six greenhouse cucumber cultivars. Age life expectancy of T. turkestani in each stage was shown by solid black circle (egg), solid white circle (larva), solid white triangle up (nymph 1), solid black triangle up (nymph 2), simple line (female) and long dash line (male) on six greenhouse cucumber cultivars. a- cultivar Puia, bcultivar Hedieh, c- cultivar Milad Jadid, d- cultivar Milad Ghadim, e- Khasib, f- Negin.